Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities

Noack, Marcus M.; Zwart, Petrus H.; Ushizima, Daniela M.; Fukuto, Masafumi; Yager, Kevin G.; Elbert, Katherine C.; Murray, Christopher B.; Stein, Aaron; Doerk, Gregory S.; Tsai, Esther R.; Li, Ruipeng; Freychet, Guillaume; Zhernenkov, Mikhail; Holman, Hoi-Ying N.; Lee, Steven; Chen, Liang; Rotenberg, Eli; Weber, Tobias; Goc, Yannick Le; Boehm, Martin; Steffens, Paul; Mutti, Paolo; Sethian, James A.

doi:10.1038/s42254-021-00345-y

Title: Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities

Journal Article · 28 July 2021 · Nature Reviews Physics

DOI: https://doi.org/10.1038/s42254-021-00345-y · OSTI ID:1810829

^[1]; Zwart, Petrus H. ^[1]; Ushizima, Daniela M. ^[2]; Fukuto, Masafumi ^[3]; Yager, Kevin G. ^[4]; Elbert, Katherine C. ^[5]; Murray, Christopher B. ^[5]; Stein, Aaron ^[4];

^[4]; Tsai, Esther R. ^[4]; Li, Ruipeng ^[3];

^[3];

^[3]; Holman, Hoi-Ying N. ^[6]; Lee, Steven ^[7]; Chen, Liang ^[6];

^[8];

^[9]; Goc, Yannick Le ^[9]; Boehm, Martin ^[9] more »

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). The Center for Advanced Mathematics for Energy Research Applications (CAMERA)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). The Center for Advanced Mathematics for Energy Research Applications (CAMERA); San Francisco State Univ., CA (United States)
Brookhaven National Lab. (BNL), Upton, NY (United States). National Synchrotron Light Source II (NSLS-II)
Brookhaven National Lab. (BNL), Upton, NY (United States)
Univ. of Pennsylvania, Philadelphia, PA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Physics
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)
Institut Laue-Langevin (ILL), Grenoble (France)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). The Center for Advanced Mathematics for Energy Research Applications (CAMERA); Univ. of California, Berkeley, CA (United States)

The execution and analysis of complex experiments are challenged by the vast dimensionality of the underlying parameter spaces. Although an increase in data-acquisition rates should allow broader querying of the parameter space, the complexity of experiments and the subtle dependence of the model function on input parameters remains daunting owing to the sheer number of variables. New strategies for autonomous data acquisition are being developed, with one promising direction being the use of Gaussian process regression (GPR). GPR is a quick, non-parametric and robust approximation and uncertainty quantification method that can be applied directly to autonomous data acquisition. We review GPR-driven autonomous experimentation and illustrate its functionality using real-world examples from large experimental facilities in the USA and France. We introduce the basics of a GPR-driven autonomous loop with a focus on Gaussian processes, and then shift the focus to the infrastructure that needs to be built around GPR to create a closed loop. Finally, the case studies we discuss show that Gaussian-process-based autonomous data acquisition is a widely applicable method that can facilitate the optimal use of instruments and facilities by enabling the efficient acquisition of high-value datasets.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1810829

Journal Information:: Nature Reviews Physics, Journal Name: Nature Reviews Physics Journal Issue: 10 Vol. 3; ISSN 2522-5820

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (48)

Phase Transformations and Structural Developments in the Radular Teeth of Cryptochiton Stelleri Wang, Qianqian; Nemoto, Michiko; Li, Dongsheng Advanced Functional Materials, Vol. 23, Issue 23 https://doi.org/10.1002/adfm.201202894	journal	January 2013
Combinatorial Mapping of Surface Energy Effects on Diblock Copolymer Thin Film Ordering Smith, Archie P.; Sehgal, Amit; Douglas, Jack F. Macromolecular Rapid Communications, Vol. 24, Issue 1 https://doi.org/10.1002/marc.200390001	journal	January 2003
High-throughput characterization of pattern formation in symmetric diblock copolymer films Smith, Archie P.; Douglas, Jack F.; Meredith, J. Carson Journal of Polymer Science Part B: Polymer Physics, Vol. 39, Issue 18 https://doi.org/10.1002/polb.1188	journal	January 2001
A comparison of the Shannon and Kullback information measures Hobson, Arthur; Cheng, Bin-Kang Journal of Statistical Physics, Vol. 7, Issue 4 https://doi.org/10.1007/BF01014906	journal	April 1973
The dynamics of cyanobacterial silicification: an infrared micro-spectroscopic investigation Benning, Liane G.; Phoenix, V. R.; Yee, N. Geochimica et Cosmochimica Acta, Vol. 68, Issue 4 https://doi.org/10.1016/S0016-7037(03)00488-5	journal	February 2004
Molecular characterization of cyanobacterial silicification using synchrotron infrared micro-spectroscopy Benning, Liane G.; Phoenix, V. R.; Yee, N. Geochimica et Cosmochimica Acta, Vol. 68, Issue 4 https://doi.org/10.1016/S0016-7037(03)00489-7	journal	February 2004
Multifunctional ToF-SIMS: combinatorial mapping of gradient energy substrates Roberson, Sonya V.; Fahey, Albert J.; Sehgal, Amit Applied Surface Science, Vol. 200, Issue 1-4 https://doi.org/10.1016/S0169-4332(02)00887-5	journal	November 2002
Hybrid genetic deflated Newton method for global optimisation Noack, Marcus M.; Funke, Simon W. Journal of Computational and Applied Mathematics, Vol. 325 https://doi.org/10.1016/j.cam.2017.04.047	journal	December 2017
Interplay of microbial communities with mineral environments in coralline algae Valdespino-Castillo, Patricia M.; Bautista-García, Andrea; Favoretto, Fabio Science of The Total Environment, Vol. 757 https://doi.org/10.1016/j.scitotenv.2020.143877	journal	February 2021
Update 2.0 to “Takin: An open-source software for experiment planning, visualisation, and data analysis”, (PII: S2352711016300152) Weber, Tobias SoftwareX, Vol. 14 https://doi.org/10.1016/j.softx.2021.100667	journal	June 2021
X-Ray Scattering Used to Map the Preferred Collagen Orientation in the Human Cornea and Limbus Aghamohammadzadeh, Hossein; Newton, Richard H.; Meek, Keith M. Structure, Vol. 12, Issue 2 https://doi.org/10.1016/j.str.2004.01.002	journal	February 2004
Nanostructure as seen by the SAXS Dubček, P. Vacuum, Vol. 80, Issue 1-3 https://doi.org/10.1016/j.vacuum.2005.07.045	journal	October 2005
Introduction to the Theory of Thermal Neutron Scattering Squires, G. L. https://doi.org/10.1017/CBO9781139107808	book	May 2012
Synchrotron IR Spectromicroscopy: Chemistry of Living Cells Holman, Hoi-Ying N.; Bechtel, Hans A.; Hao, Zhao Analytical Chemistry, Vol. 82, Issue 21 https://doi.org/10.1021/ac100991d	journal	November 2010
Catalysis of PAH Biodegradation by Humic Acid Shown in Synchrotron Infrared Studies Holman, Hoi-Ying N.; Nieman, Karl; Sorensen, Darwin L. Environmental Science & Technology, Vol. 36, Issue 6 https://doi.org/10.1021/es0157200	journal	March 2002
Characterization of Metal−Cyanobacteria Sorption Reactions: A Combined Macroscopic and Infrared Spectroscopic Investigation Yee, Nathan; Benning, Liane G.; Phoenix, Vernon R. Environmental Science & Technology, Vol. 38, Issue 3 https://doi.org/10.1021/es0346680	journal	February 2004
Creating Controlled Thickness Gradients in Polymer Thin Films via Flowcoating Davis, Raleigh L.; Jayaraman, Sahana; Chaikin, Paul M. Langmuir, Vol. 30, Issue 19 https://doi.org/10.1021/la501247x	journal	May 2014
High-Throughput Measurement of Polymer Blend Phase Behavior Meredith, J. Carson; Karim, Alamgir; Amis, Eric J. Macromolecules, Vol. 33, Issue 16 https://doi.org/10.1021/ma0004662	journal	August 2000
Combinatorial Materials Science for Polymer Thin-Film Dewetting Meredith, J. Carson; Smith, Archie P.; Karim, Alamgir Macromolecules, Vol. 33, Issue 26 https://doi.org/10.1021/ma001298g	journal	December 2000
Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm Probst, Alexander J.; Holman, Hoi-Ying N.; DeSantis, Todd Z. The ISME Journal, Vol. 7, Issue 3 https://doi.org/10.1038/ismej.2012.133	journal	November 2012
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon The ISME Journal, Vol. 6, Issue 9 https://doi.org/10.1038/ismej.2012.59	journal	June 2012
Unconventional superconductivity in magic-angle graphene superlattices Cao, Yuan; Fatemi, Valla; Fang, Shiang Nature, Vol. 556, Issue 7699 https://doi.org/10.1038/nature26160	journal	March 2018
A Kriging-Based Approach to Autonomous Experimentation with Applications to X-Ray Scattering Noack, Marcus M.; Yager, Kevin G.; Fukuto, Masafumi Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-48114-3	journal	August 2019
Advances in Kriging-Based Autonomous X-Ray Scattering Experiments Noack, Marcus M.; Doerk, Gregory S.; Li, Ruipeng Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-57887-x	journal	January 2020
Autonomous materials discovery driven by Gaussian process regression with inhomogeneous measurement noise and anisotropic kernels Noack, Marcus M.; Doerk, Gregory S.; Li, Ruipeng Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-74394-1	journal	October 2020
Autonomous adaptive data acquisition for scanning hyperspectral imaging Holman, Elizabeth A.; Fang, Yuan-Sheng; Chen, Liang Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-01385-3	journal	November 2020
Bayesian statistics and modelling van de Schoot, Rens; Depaoli, Sarah; King, Ruth Nature Reviews Methods Primers, Vol. 1, Issue 1 https://doi.org/10.1038/s43586-020-00001-2	journal	January 2021
Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue Liu, Jiliang; Costantino, Isabel; Venugopalan, Nagarajan Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep33079	journal	September 2016
Generating thickness gradients of thin polymer films via flow coating Stafford, Christopher M.; Roskov, Kristen E.; Epps, Thomas H. Review of Scientific Instruments, Vol. 77, Issue 2 https://doi.org/10.1063/1.2173072	journal	February 2006
Versatile platform for creating gradient combinatorial libraries via modulated light exposure Berry, Brian C.; Stafford, Christopher M.; Pandya, Mayur Review of Scientific Instruments, Vol. 78, Issue 7 https://doi.org/10.1063/1.2755729	journal	July 2007
Electrospray deposition tool: Creating compositionally gradient libraries of nanomaterials Toth, Kristof; Osuji, Chinedum O.; Yager, Kevin G. Review of Scientific Instruments, Vol. 91, Issue 1 https://doi.org/10.1063/1.5129625	journal	January 2020
Real-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response Holman, H. -Y. N.; Wozei, E.; Lin, Z. Proceedings of the National Academy of Sciences, Vol. 106, Issue 31 https://doi.org/10.1073/pnas.0902070106	journal	June 2009
Real-Time Characterization of Biogeochemical Reduction of Cr(VI) on Basalt Surfaces by SR-FTIR Imaging Geomicrobiology Journal, Vol. 16, Issue 4 https://doi.org/10.1080/014904599270569	journal	November 1999
Instrumentation for In situ/Operando X-ray Scattering Studies of Polymer Additive Manufacturing Processes Wiegart, L.; Doerk, G. S.; Fukuto, M. Synchrotron Radiation News, Vol. 32, Issue 2 https://doi.org/10.1080/08940886.2019.1582285	journal	March 2019
ThALES—Three Axis Low Energy Spectroscopy for highly correlated electron systems Boehm, M.; Steffens, P.; Kulda, J. Neutron News, Vol. 26, Issue 3 https://doi.org/10.1080/10448632.2015.1057050	journal	July 2015
K-means-driven Gaussian Process data collection for angle-resolved photoemission spectroscopy Melton, Charles N.; Noack, Marcus M.; Ohta, Taisuke Machine Learning: Science and Technology, Vol. 1, Issue 4 https://doi.org/10.1088/2632-2153/abab61	journal	October 2020
Small-angle scattering in materials science - a short review of applications in alloys, ceramics and composite materials Fratzl, Peter Journal of Applied Crystallography, Vol. 36, Issue 3 https://doi.org/10.1107/S0021889803000335	journal	April 2003
Periodic lattices of arbitrary nano-objects: modeling and applications for self-assembled systems Yager, Kevin G.; Zhang, Yugang; Lu, Fang Journal of Applied Crystallography, Vol. 47, Issue 1 https://doi.org/10.1107/S160057671302832X	journal	December 2013
Computational Strategies to Increase Efficiency of Gaussian-Process-Driven Autonomous Experiments Noack, Marcus; Zwart, Petrus 2019 IEEE/ACM 1st Annual Workshop on Large-scale Experiment-in-the-Loop Computing (XLOOP) https://doi.org/10.1109/XLOOP49562.2019.00006	conference	November 2019
Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill: Enrichment of oil degraders from Gulf of Mexico Baelum, Jacob; Borglin, Sharon; Chakraborty, Romy Environmental Microbiology, Vol. 14, Issue 9 https://doi.org/10.1111/j.1462-2920.2012.02780.x	journal	May 2012
From diffraction to imaging: New avenues in studying hierarchical biological tissues with x-ray microbeams (Review) Paris, Oskar Biointerphases, Vol. 3, Issue 2 https://doi.org/10.1116/1.2955443	journal	June 2008
Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria Hazen, Terry C.; Dubinsky, Eric A.; DeSantis, Todd Z. Science, Vol. 330, Issue 6001 https://doi.org/10.1126/science.1195979	journal	August 2010
The Stomatopod Dactyl Club: A Formidable Damage-Tolerant Biological Hammer Weaver, J. C.; Milliron, G. W.; Miserez, A. Science, Vol. 336, Issue 6086 https://doi.org/10.1126/science.1218764	journal	June 2012
Band structure and many body effects in graphene Bostwick, A.; Ohta, T.; McChesney, J. L. The European Physical Journal Special Topics, Vol. 148, Issue 1 https://doi.org/10.1140/epjst/e2007-00220-x	journal	September 2007
The impact of alterations in lignin deposition on cellulose organization of the plant cell wall Liu, Jiliang; Kim, Jeong Im; Cusumano, Joanne C. Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0540-z	journal	June 2016
Bayesian Optimization Frazier, Peter I. Recent Advances in Optimization and Modeling of Contemporary Problems https://doi.org/10.1287/educ.2018.0188	book	October 2018
Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba Valdespino-Castillo, Patricia M.; Hu, Ping; Merino-Ibarra, Martín Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00510	journal	April 2018
The impact of alterations in lignin deposition on cellulose organization of the plant cell wall Liu, Jiliang; Kim, Jeong; Cusumano, Joanne Figshare https://doi.org/10.6084/m9.figshare.c.3599612	collection	January 2016

Similar Records

Autonomous materials discovery driven by Gaussian process regression with inhomogeneous measurement noise and anisotropic kernels

Journal Article · 2020 · Scientific Reports · OSTI ID:1678746

Noack, Marcus M.; Doerk, Gregory S.; Li, Ruipeng; +4 more

Mathematical nuances of Gaussian process-driven autonomous experimentation

Journal Article · 2023 · MRS Bulletin · OSTI ID:1959266

Noack, Marcus M.; Reyes, Kristofer G.

Toward implementing autonomous adaptive data acquisition for scanning hyperspectral imaging of biological systems

Journal Article · 2023 · Applied Physics Reviews · OSTI ID:2564757

Holman, Elizabeth A.; Krishnan, Harinarayan; Holman, Derek R.; +2 more

Related Subjects

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Title: Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities

Citation Formats

References (48)

Similar Records

Related Subjects